Saw this over in general discussions, original post relates to an older LS, but this has worked for me on my 59 plate IS250:
All four doors creaked considerably when going over bumps etc. I tried spraying silicone on the rubbers, it worked for a couple of hours and then came back. I discovered it happens a lot to BMW and Audi.
Various forums claim to have the answers, but one in particular from the States worked. The person posting said to clean all of the rubber areas, including the window rubber with undiluted dish washing liquid, as they say it's a build up of cleaning/lubricating products that cause it. Also to clean the bodywork in the appropriate areas.